title: IFNARKO-mice_IRF1KO-MC38, scRNA-Seq

city: los angeles

first: Prabhat

middle: Kumar

last: Purbey

state: California

address: 675 Charles E. Young Drive South

department: MIMG

institute: UCLA

data_processing:
scRNA-seq libraries were sequenced paired-end at 100 cycle in an Illumina NovaSeq 6000 S1 platform.
Sequencing data were demultiplexed in Basespace (Illumina), and mapped, barcode collapsed, and filtered in the Cell Ranger (V6.0.2) software (10x Genomics). Reads were mapped to the mm10 Refseq mouse reference transcriptome.
FASTQ files were used to aligned to the mm10 mouse reference genome using Cell ranger count with default settings.
The output from Cellranger count, a raw sparse matrix with digital expression of cell barcodes by genes was used for downstream analysis in R using  Seurat v 4.1. Quality control measures were imposed, which excluded cells with fewer than 200 detected genes or more than 20% mitochondrial reads. To identify and remove doublets, the cell matrix was processed by DoubletFinder (https://github.com/chris-mcginnis-ucsf/DoubletFinder). The filtered dataset underwent normalization and scaling using the SCTransform method within the Seurat package (version 4.1), which stabilizes variance across features. Integration of multiple scRNA-seq datasets was carried out by employing the Harmony algorithm. The RunHarmony function was invoked with dims = 1:50 to perform the integration on the scaled and normalized expression data of the selected 3,000 features. Post-integration, we conducted principal component analysis (PCA) on the harmonized data, followed by the construction of a shared nearest neighbor (SNN) graph with the top 20 principal components. Clusters were identified using the Louvain algorithm with a resolution of 0.5 (optimized after trying several resolution).  For visualization, we employed the Harmony embedding technique, which facilitated the creation of a Uniform Manifold Approximation and Projection (UMAP) plot to display the data in a two-dimensional space. Clusters were annotated based on expression of known cell type-specific markers using literature and various databases (PanglaoDB, Enrichr, human protein atlas) and differentially expressed genes in distinct clusters. Genes were considered differentially expressed based on Wilcoxon rank sum test with an adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: "barcodes.tsv.gz" is produced by cellranger count, is a compressed TSV (Tab-Separated Values) file, which contains a list of unique barcodes used to identify individual cells. This is one of the 3 files required for analysis with  Seurat package in R.
Supplementary files format and content: "features.tsv.gz" is produced by cellranger count, is a compressed TSV file, which contains information about the genes/ transcripts. This is one of the 3 files required for analysis with  Seurat package in R.
Supplementary files format and content: "matrix.mtx.gz", is produced by cellranger count, is a compressed MTX (Matrix Market) file, contains the sparse matrix of gene expression counts where rows represent genes, columns represent cell barcodes, and the values are the number of reads that map to each gene for each cell. This is one of the 3 files required for analysis with  Seurat package in R.

source_name: subcutaneous tumor

growth_protocol: WT or IRF1-KO MC38 cancer cells were subcutaneously grown in WT or IFNAR-KO mice for 12 days before harvest of tumor for single-cell dissociation for sc-RNA-Seq

extract_protocol:
on day12 were chopped into small pieces (2-4 mm size) with a scalpel before dissociation with Miltenyi’s gentle MACS enzyme mix (mouse tumor dissociation kit, # 130-096-730) in a Miltenyi GentleMACS Octo Dissociator (Miltenyi Biotec Inc., San Diego, CA) with pre- set 37C_mTDK_1 protocol. After dissociation, the cell suspension was filtered through 70uM MACS smart strainer and dead cells were removed using dead cell removal kit (Miltenyi Biotec Inc.,). Cells were counted using Countess II Automated Cell Counter (Thermo Fisher Scientific) and hemocytometer for cell concentration and viability using Trypan Blue stain 0.4% (Invitrogen).  Viability of cells was above 90% and 10X genomics recommendended cells were used to target about 10,000 cells.
Single cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer’s instructions.

value: subcutaneous tumor

value: mixed population

value: IFNAR-mice and IRF1KO-tumor

value: No treatment


title: AGI881_P1_H03, scRRBS (multi-omics)

status: Public on May 01 2024

type: SRA

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

country: USA

institute: Massachusetts General Hospital

description: scRRBS_mouse_multiomics_processed_CpG.tsv

library_source: genomic

data_processing:
Analysis of single cell DNA methylation data was performed based on the methods detailed in Chaligne et al 2021. After demultiplexing, reads were mapped to the mm10 genome and cells with at least 25,000 CpG sites, 1 million reads and mapping efficiency greater than 30% were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: tsv

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse cell line single cell, IDHmutant mouse glioma cell

extract_protocol:
IdhR132H mouse glioma cells were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks.  The treated cells were washed with cold PBS and then stained with 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies) for 30 min at 4°C. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter) and  640nm (TO-PRO-3, 670/14 filter). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets. Calcein AM positive and TO-PRO-3 negative live cells were sorted into 96 wells containing TCL buffer (QIAGEN) for the single-cell multi-omics experiment.
The single-cell plates for the mouse glioma cells treaded by AG-881 or DMSO were profiled by the joint single-cell RRBS and whole transcriptome amplification (Smart-seq2) protocol. The library preparation and sequencing were performed as previously described (Chaligne et al, 2021). Single enzyme digestion (MspI) was used to enrich CpG dense regions in single-cell RRBS.

tag: tissue

tag: treatment (idhi)

value: Yes


title: MDM_HIV_BaL_d4_biol_rep2

city: Cincinnati

first: Jason

last: Hammonds

state: Ohio

address: 3333 Burnet Ave

department: Infectious Diseases

institute: Cincinnati Children's Hospital Medical Center

library_source: transcriptomic

data_processing:
Raw reads from purified RNA of cultured macrophages/microglia were processed using the nf-core/rnaseq pipeline version 3.4
Adapter sequences and low-quality reads were filtered and trimmed using FastQ and Trim Galore. Filtered reads were mapped to the human GRCh38 reference genome version 108 using STAR
Duplicate reads were removed using MarkDuplicates. Next, Salmon [10.1038/nmeth.4197] was used to generate a count matrix from genes with mapped reads.
Assembly: hg38
Supplementary files format and content: Transcripts counts table text file
Supplementary files format and content: tab-delimited text file includes raw counts for each sample to include those present in principle component analysis of Figure 1A.
Supplementary files format and content: tab-delimited text file included raw counts for each sample
Supplementary files format and content: tab-delimited text file includes metadata for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

growth_protocol: Detailed methods for isolation, maturation and maintenance of human iMGLs provided in Stem Cell-derived Microglia Exhibit HAND Gene Expression Signature Immediately Upon Infection with HIV-1.

extract_protocol:
Total cellular RNA was extracted from 1 x10^6 iMGLs using QIAGEN RNeasy Mini Kit following standard operating procedures.
For high through-put RNA sequencing, 300 ng of RNA per sample was used to construct RNAseq libraries employing Illumina TruSeq mRNA standard protocols.

treatment_protocol: Infection with primary HIV-1 isolate BaL at an MOI of 0.25.

value: Whole blood

tag: cell line

value: Peripheral blood monocytes (PBMs)

tag: cell type

value: Monocyte-derived macrophages (MDMs)

tag: time

value: Day 4

tag: treatment

value: HIV-1 BaL Infected


title: Lx761c-Comb3

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

data_processing:
In-line UMI sequences were trimmed from the sequencing reads with Marianas (https://github.com/mskcc/Marianas) and aligned to human GRCh38 genome using STAR 2.7.0 (https://github.com/alexdobin/STAR) [25] with Ensembl v92 gene annotation.
Hybrid selection-specific metrics and alignment metrics were calculated for the BAM files using CalculateHsMetrics and CollectRnaSeqMetrics, respectively, from Picard Toolkit (https://github.com/broadinstitute/picard) to determine the quality of the capture.
We quantified RNA-seq reads with Kallisto v.0.45.053 to obtain transcript counts and abundances.
Transcript per million (TPM) normalization by size factors was done from Kallisto output files using Sleuth v0.30.0 run in gene mode.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with TPM values over all genes for each sample.

source_name: :Lung

extract_protocol:
Frozen tissues were weighed and homogenized in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water.
Fresh cell pellet or frozen tumor samples were shipped to GENEWIZ for RNA isolation, library preparation, and RNA sequencing. Total RNA was extracted using the RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). RNA samples and sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Sequencing libraries were clustered on one flowcell lane and then loaded on the Illumina HiSeq instrument (4000 or equivalent) (RRID: SCR_020127) according to manufacturer’s instructions. Samples were sequenced using a 2x150bp paired end (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bclfiles) was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software (RRID: SCR_015058). One mismatch was allowed for index sequence identification.

value: :Lung

value: SCLC

tag: genotype

value: Cisplatin+simurosertib


title: WT-mice_IRF1KO-MC38_set2, scRNA-Seq

library_source: transcriptomic single cell

molecule: polyA RNA

value: WT-mice and IRF1KO-tumor


title: AGI881_P1_H02, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: AGI881_P1_H01, scRRBS (multi-omics)


title: MDM_HIV_BaL_d4_biol_rep1


title: WT-mice_WT-MC38_set2, scRNA-Seq

value: WT-mice and WT-tumor


title: Lx761c-Comb1


title: MDM_HIV_BaL_d2_biol_rep3

value: Day 2


title: AGI881_P1_G12, scRRBS (multi-omics)


title: Lx33-Sim3

value: Simurosertib


title: Lx33-Sim4


title: WT-mice_IRF1KO-MC38_set1, scRNA-Seq

value: subcutaneous tumor

value: mixed population


title: MDM_HIV_BaL_d2_biol_rep1


title: AGI881_P1_H10, scRRBS (multi-omics)


title: AGI881_P1_H05, scRRBS (multi-omics)


title: NSD2fl/fl

city: 北京市

first: YIJIA

last: ZHANG

address: 和平街道

country: China

institute: Beijing University of Chemical Technology

description: WT

data_processing:
*library strategy: CUT&Tag
The raw data (raw reads) generated in high-throughput sequencing are fastq format sequences. In order to obtain high-quality reads that can be used for subsequent analysis, further quality filtering of raw reads is required. First, use the fatsp software to remove adapters, and then filter out low-quality bases and N bases or low-quality reads, and finally obtain high-quality clean reads.
Use Bowtie2 to align the clean reads to the reference genome of the experimental species, and evaluate the sample situation through the genome and gene alignment rate. The parameters used are the default parameters.
To evaluate the IP quality of CUT&Tag experiments, we use strand cross-correlation (SCC) analysis. Theoretically, the reads obtained by sequencing will eventually be distributed approximately equally between the positive and negative strands.
Deeptools software is used to draw a FingerPrint diagram to show the distinction between the CUT&Tag enriched signal and the background signal, and at the same time, the ChIP signal type (narrow peak or broad peak) can be determined.
The sequencing data were compared with the reference genome, and then binding peak detection was performed using SEACR [4] software. Use chipseeker software to annotate the Peaks of each sample on a sample basis, obtain the genes and gene information corresponding to the Peaks, and make statistics on the annotation results.
Use the MEME-ChIP suite to analyze and detect the Motif sequence in the peak sequence, and use Tomtom software to compare the obtained Motif sequence with the known Motif database, and use the known Motif to annotate it accordingly.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

source_name: colon

extract_protocol:
Colon tissue was separated from mice, cleaned, and quickly stored in a special preservation solution. CUT&Tag library construction using the kit Hyperactive TM In-Situ ChIP Library Prep Kit for Illumina (Cat. No. TD901-TD902, Vazyme Biotech Co., Ltd)
Concanavalin A-coated magnetic beads (ConA beads) were used to bind the cells, and the nonionic detergent digitonin (Digitonin) was used to permeabilize the cell membrane; the cells bound to the magnetic beads were sequentially Incubate with (enter target protein name) primary antibody (enter primary antibody product number and company), secondary antibody and Protein A/Protein G fused with Tn5 transposon (Hyperactive pA/pG-Tn5 Transposon), so that with Protein A/ The Protein G-fused Tn5 transposon precisely targets and cuts the DNA sequence near the target protein; when Tn5 cuts, it will add P5 and P7 adapter sequences to both ends of the cut fragment, and use P5 and P7 primers for PCR amplification. After the purified sequencing library passed the quality inspection of Agilent 2100 Bioanalyzer, the Illumina NovaSeq6000 sequencing platform was used for high-throughput sequencing to generate 150 bp paired-end data for subsequent analysis.

value: colon

tag: chip-antibody

value: H3K36me2 (Proteintech, A22087)

value: HFCD


title: Lx33-Sim2


title: MDM_HIV_BaL_d1_biol_rep3

value: Whole blood

value: Peripheral blood monocytes (PBMs)

value: Day 1


title: AGI881_P1_G10, scRRBS (multi-omics)

value: Yes


title: NSD2∆IE


title: MDM_HIV_BaL_d1_biol_rep2

value: Monocyte-derived macrophages (MDMs)

value: HIV-1 BaL Infected


title: Lx33-Sim1

value: :Lung

value: SCLC


title: AGI881_P1_G09, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: Lx33-Ctrl4

value: Control


title: MDM_HIV_BaL_d1_biol_rep1


title: Lx761c-Comb2

value: Cisplatin+simurosertib


title: NSD2∆IE RNA-seq 3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads， clean reads for each sample were retained for subsequent analyses
The clean reads were mapped to the reference genome using HISAT2. FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4.
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the instructions.
RNA purity and quantification were characterized using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA) and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Intestinal-specific NSD2 knockout mice (NSD2∆IE) and controls (NSD2fl/fl) were treated with a 16-week HFCD diet

value: 16 weeks of HFCD


title: AGI881_P1_G08, scRRBS (multi-omics)


title: NSD2∆IE RNA-seq 2


title: MDM_HIV_BaL_d0_biol_rep3

value: Day 0


title: MDM_HIV_BaL_d2_biol_rep2

value: Day 2


title: Lx33-Ctrl3


title: AGI881_P1_H11, scRRBS (multi-omics)


title: WT-mice_WT-MC38_set1, scRNA-Seq

value: subcutaneous tumor

value: mixed population

value: WT-mice and WT-tumor

value: No treatment


title: Lx33-Ctrl2


title: MDM_HIV_BaL_d0_biol_rep2

value: Whole blood

value: Peripheral blood monocytes (PBMs)


title: NSD2∆IE RNA-seq 1

value: colon


title: AGI881_P1_G05, scRRBS (multi-omics)

value: Yes


title: Lx33-Ctrl1


title: NSD2fl/fl RNA-seq 2


title: MDM_Uninfected_d8

value: Monocyte-derived macrophages (MDMs)

value: Day 8


title: NSD2fl/fl RNA-seq 3


title: Lx33-Comb3

value: :Lung

value: SCLC


title: MDM_Uninfected_d6

value: Day 6


title: AGI881_P1_G04, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: sequenced matrices from spine_KO_day250

city: Cambridge

first: Francesco

last: Limone

state: Massachusetts

address: 7 divinity avenue, Bauer Laboratory 008

institute: harvard university

description:
spine_KO_day250
10x Genomics

data_processing:
Raw sequence data was demultiplexed and aligned followingthe standard Drop-Seq protocol (Macosko et al., 2015)
Count matrices were generated for each sample, a combined UMI matrix was generated using merge(). This matrix was first filtered for number of genes (nFeature) and percentage of mitochondrial and ribosomal genes (400< nFeature_RNA < 4000, percent.mito < 25, percent.RPS < 15, percent.RPL < 15) and then normalized and scaled as per manual using Seurat (v3.0.1)
Assembly: GRCm38 reference
Supplementary files format and content: processed unfiltered matrices

source_name: spine

extract_protocol:
For dissociation of brain and spinal cord tissue for single cell sequencing, 2 ml glasspipette tips was used tohomogenize the tissue and dissociated with papain (Worthington) supplemented with DNAse in Ca2+-free serum-free Earle’s Balanced Salt Solution pre-heated to 37C.Tissue dissociated at 37C for 25 min, with homogenization after 10 minutes using 1 mL plastic tip. After 25 min the tissue was homogenized again with 1 mL plastic tip andpassed through 70 um filter and Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% Fetal Bovine Serum added, spun at 300g for 10 mins. Cells subjected to myelin removal beads (Miltenyi), counted, diluted in Ca2+ -free Hank’s Balanced Salt Solution with 0.5% Bovine Serum Albuminand loaded into a Chromium Single Cell 3’ Chip (10X Genomics) and processed follow manufacturer’s instructions.
Sequencing libraries were prepared with the Chromium Single Cell 3’ library and Gel Bead kit v2 (10X Genomics). Libraries were sequenced on a Nova-seq 6000.Reads were aligned to the mouse genome assembly GRCm38.

value: spine

value: KO


title: AGI881_P1_H06, scRRBS (multi-omics)


title: NSD2fl/fl RNA-seq 1

value: 16 weeks of HFCD


title: Lx33-Comb2

value: Cisplatin+simurosertib


title: Lx33-Comb4


title: sequenced matrices from spine_KO_day100

description:
spine_KO_day100
10x Genomics


title: AGI881_P1_H09, scRRBS (multi-omics)


title: AGI881_P1_G01, scRRBS (multi-omics)


title: MDM_Uninfected_d2

value: Day 2


title: Lx33-Comb1


title: sequenced matrices from spine_KO_day50

description:
spine_KO_day50
10x Genomics


title: MDM_Uninfected_d1

value: Day 1


title: AGI881_P1_F04, scRRBS (multi-omics)


title: sequenced matrices from spine_WT_day250

description:
spine_WT_day250
10x Genomics

value: WT


title: SKOV3_sh_KLF5_3

city: Jinan

first: shourong

last: wang

address: No. 107, Wenhua West Road, Lixia District, Jinan City, Shandong Province

institute: Qilu Hospital，Shandong University

data_processing:
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each 2 gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: hg38
Supplementary files format and content: spreadsheet file include FPKM values for each sample

source_name: ovary

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufac_x0002_turer’s protocol.mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

value: ovarian cancer cell

value: KLF5 knockdown


title: MDM_HIV_BaL_d0_biol_rep1

value: Whole blood

value: Peripheral blood monocytes (PBMs)

value: Day 0


title: AGI881_P1_F03, scRRBS (multi-omics)

value: Yes


title: AGI881_P1_H08, scRRBS (multi-omics)


title: sequenced matrices from spine_WT_day100

description:
spine_WT_day100
10x Genomics


title: AGI881_P1_F02, scRRBS (multi-omics)


title: Lx33-Cis2

value: :Lung

value: SCLC

value: Cisplatin


title: Lx33-Cis3


title: SKOV3_sh_KLF5_1


title: SKOV3_sh_KLF5_2


title: MDM_Uninfected_d4

value: Monocyte-derived macrophages (MDMs)

value: Day 4


title: SKOV3_NC_3


title: Lx33-Cis4


title: sequenced matrices from spine_WT_day50

description:
spine_WT_day50
10x Genomics

value: spine


title: AGI881_P1_F11, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: sequenced matrices from brain_KO_day250

description:
brain_KO_day250
10x Genomics

source_name: brain

value: brain

value: KO


title: Lx33-Cis1


title: sequenced matrices from brain_KO_day100

description:
brain_KO_day100
10x Genomics


title: AGI881_P1_E12, scRRBS (multi-omics)


title: H146-Sim4

value: Simurosertib


title: SKOV3_NC_2

value: ovary

value: WT


title: H146-Sim3


title: sequenced matrices from brain_KO_day50

description:
brain_KO_day50
10x Genomics


title: AGI881_P1_E11, scRRBS (multi-omics)


title: H146-Sim2


title: SKOV3_NC_1

value: ovarian cancer cell


title: AGI881_P1_F01, scRRBS (multi-omics)


title: sequenced matrices from brain_WT_day250

description:
brain_WT_day250
10x Genomics


title: AGI881_P1_F10, scRRBS (multi-omics)


title: MDA-MB-468, DETA/NO, 10 days, rep3

city: Chicago

first: Douglas

middle: David

last: Thomas

state: Illinois

address: 900 S Ashland Ave

department: Pharmaceutical Sciences

institute: University of Illinois Chicago

description: re-analysis of GSM7526955

data_processing:
Reads were aligned to hg38 using STAR 2.5.2a (Gencode_human/release_22).
Bams were sorted using samtools.
Gene counts were generated using HTSeq (Gencode_human/release_22).
Differential expression analysis was completed using edgeR v3.40.2.
Gene Set Enrichment Analysis was completed using in-house OmicPath and edgeR.
Assembly: hg38

source_name: triple-negative breast cancer

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with 10% qualified fetal bovine serum (FBS; Gibco) and 1% penicillin/streptomycin (P/S; Gibco). All cells were cultured at 37°C in 5% CO2.

extract_protocol:
Total RNAs were isolated using the RNAqueous™-4PCR kit (Ambion) and treated with DNase I (Ambion) to avoid genomic DNA contaminations.
Libraries were prepared with KAPA RNA Hyper Prep kit (Roche).

treatment_protocol: Cells were first plated with a density of 1.5x10^6 cells into 100 mm dishes. After 4h of cell adherence, 100 uM of DETA/NO was added to the media and cells were allowed to grow for 48h. At this time, cells were collected with trypsin (Gibco), pooled according to each replicate, counted, and re-plated at the same starting density of 1.5x10^6 cells into new 100 mm dishes. This was repeated every 48 h for a total of 10 days of DETA/NO treatment.

value: triple-negative breast cancer

value: epithelial

value: 100 uM DETA/NO


title: sequenced matrices from brain_WT_day100

description:
brain_WT_day100
10x Genomics


title: H146-Ctrl4

value: Control


title: AGI881_P1_E10, scRRBS (multi-omics)

value: Yes


title: MDA-MB-468, DETA/NO, 10 days, rep2

description: re-analysis of GSM7526953


title: sequenced matrices from brain_WT_day50

description:
brain_WT_day50
10x Genomics


title: AGI881_P1_E08, scRRBS (multi-omics)


title: MDA-MB-468, DETA/NO, 10 days, rep1

description: re-analysis of GSM7526952


title: H146-Ctrl2

value: :Lung

value: SCLC


title: MDA-MB-468, Control, 10 days, rep3

description: re-analysis of GSM7526951

value: untreated


title: H146-Ctrl1


title: AGI881_P1_E07, scRRBS (multi-omics)


title: N10,biol rep2,D6,snRNAseq

city: beijing

first: qian

last: chen

address: No. 5, Panjiayuan South

institute: PUMC

description: 10x Genomics

data_processing:
Fastp was used to perform basic statistics on the quality of the raw reads.Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (cellranger-6.0.0) using default parameters.
Cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data.
The Seurat package was used to normalise data, dimensionality reduction,clustering,differential expression. we used Seurat alignment method canonical correlation analysis (CCA).
Gene Ontology (GO) and KEGG enrichment analysis of marker genes was implemented by the  clusterProfiler R package.Reactome pathway-based analysis of marker genes was implemented by the  ReactomePA R package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Freshly liver tissues collected from Ifnar1 knock-out mice were washed with pre-cooled phosphate buffer saline (PBS) buffer to remove excess blood. Then weigh the liver tissue and cool it quickly in liquid nitrogen.Next,transfer it to −80℃ refrigerator for storage.Single-nucleus suspensions were generated according 10x Genomics Nuclei Isolation from Cell Suspensions Protocols.
The cell suspension was loaded into Chromium microfluidic chips with 3’ V3.1 chemistry and barcoded with a 10× Chromium Controller (10X Genomics).

value: liver

tag: group


title: N10,biol rep1,D6,snRNAseq

description: 10x Genomics


title: H146-Comb4

value: Cisplatin+simurosertib


title: NGC,biol rep3,D6,snRNAseq

description: 10x Genomics

value: NGC


title: AGI881_P1_F09, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: AGI881_P1_E06, scRRBS (multi-omics)


title: MDA-MB-231, DETA/NO, 10 days, rep3

description: re-analysis of GSM7526968


title: H146-Comb3


title: AGI881_P1_E05, scRRBS (multi-omics)


title: H146-Comb2


title: H146-Sim1


title: NGC,biol rep2,D6,snRNAseq

description: 10x Genomics


title: MDA-MB-231, DETA/NO, 10 days, rep2

description: re-analysis of GSM7526967


title: H146-Ctrl3


title: AGI881_P1_E09, scRRBS (multi-omics)


title: AGI881_P1_E04, scRRBS (multi-omics)


title: H146-Comb1


title: MDA-MB-231, DETA/NO, 10 days, rep1

description: re-analysis of GSM7526966


title: NGC,biol rep1,D6,snRNAseq

description: 10x Genomics


title: Uninfected,biol rep3,D6,snRNAseq

description: 10x Genomics

value: uninfected


title: N10,biol rep3,D6,snRNAseq

description: 10x Genomics


title: AGI881_P1_F07, scRRBS (multi-omics)


title: MDA-MB-231, Control, 10 days, rep3

description: re-analysis of GSM7526965


title: MDA-MB-468, Control, 10 days, rep2

description: re-analysis of GSM7526950


title: MDA-MB-468, Control, 10 days, rep1

description: re-analysis of GSM7526949


title: H146-Cis2

value: Cisplatin


title: AGI881_P1_E02, scRRBS (multi-omics)


title: MDA-MB-231, Control, 10 days, rep2

description: re-analysis of GSM7526964


title: Uninfected,biol rep2,D6,snRNAseq

description: 10x Genomics


title: H146-Cis1


title: AGI881_P1_F06, scRRBS (multi-omics)


title: Uninfected,biol rep1,D6,snRNAseq

description: 10x Genomics


title: AGI881_P1_D12, scRRBS (multi-omics)


title: MDA-MB-231, Control, 10 days, rep1

description: re-analysis of GSM7526962


title: MDA-MB-468 5mC5hmC, DETA/NO, 10 days, rep2

data_processing:
MultiQC was used to assess read quality.
Sequences were trimmed using TrimGalore.
Reads were aligned to hg38 using bowtie2 within Bismark (mapping efficiency ~62%) to count 5mC and 5hmC marks in a CpG context.
Methylation analysis was performed using Bismark and Rnbeads.
Differential methylation analysis was performed using RnBeads, Dnmtools, and MethylKit.
Assembly: hg38
Supplementary files format and content: .bedgraph

extract_protocol:
Genomic DNA was extracted and purified from cells using the DNEasy Blood & Tissue kit (QIAGEN) with RNase step.
The libraries were prepared with the Ovation® RRBS Methyl-Seq with TrueMethyl® oxBS from Tecan.


title: FBC.Listeria

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1
Data analysis was performed using Seurat v4.1 pipeline. Low-quality cells were defined as those with less than 500 or more than 3000 unique genes, or those with >10% mitochondrial gene reads and were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: SLO, spleen

extract_protocol:
Lymphocytes were prepared by mechanical disruption (SLO, spleen), followed by staining with floursecent antibodies and tetramers, hashing with Totalseq-C antibodies against MHCI and CD45,  and flow sorting tetramer positive T cells into DMEM2%FCS
Libraries were prepared according to 10x5'v2 protocols

value: SLO, spleen

value: T cells

tag: strain

tag: Sex

value: Male

value: None, Listeria monocytogenes

tag: hashids

value: TotalSeq C1-9


title: GEX.Listeria

description: 10x lane of 8 individually hashed SLO and 1 spleen samples. Listeria samples were each at different timepoints of infection; spleen sample was an experimental control


title: Combo2 (dataset 2)

source_name: Prostate

value: Prostate

value: DKO 22PC

value: Prostate adenocarcinoma

value: TP53/RB1 KO

value: Enzalutamide+Simurosertib


title: AGI881_P1_D04, scRRBS (multi-omics)

value: Yes


title: Combo3 (dataset 2)


title: IDHmut glioma, combo-3, Day9

city: shanghai

first: Giero

last: Zhang

state: Shanghai

address: dong an road

institute: Fudan university

data_processing:
The low-quality reads were filtered out by FastQC, and the high-quality reads for each sample were aligned to the mm10 reference genome by Hisat2. The expression level of coding genes was calculated by StringTie with Transcripts Per Kilobase Million (TPM) methods, with annotation collected from UCSC (https://genome.ucsc.edu/). Then we calculated differential expression genes (DEGs) between each group using DESeq2.
Assembly: mm10
Supplementary files format and content: Processed data file is the gene expression profile as xlsx format. The expression value was processed as TPM for subsequent analysis.

source_name: Brain

extract_protocol:
We subjected tumor samples after 9 days treatments, and sent to Keymed Biosciences Inc. for downstream RNA sequencing. In brief, following RNA isolation with TRIzol, a total amount of 2 μg RNA per sample was used as input material for library preparations.
Sequencing libraries were generated per sample with the NEBNext UltraTM RNA Library Prep Kit for Illumina (#E7530L, NEB, USA) according to the manufacturer’s instructions, and subjected to deep sequencing with an Illumina sequencer NovaSeq 6000.

value: Brain

value: Glioma cells

value: IDH-mutant

value: lenvatinib+veliparib


title: AGI881_P1_D05, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: MDA-MB-468 5mC, DETA/NO, 10 days, rep2

value: triple-negative breast cancer

value: epithelial

value: 100 uM DETA/NO


title: IDHmut glioma, combo-2, Day9


title: MDA-MB-468 5mC5hmC, DETA/NO, 10 days, rep1


title: Simurosertib2 (dataset 2)

value: Simurosertib


title: Simurosertib3 (dataset 2)


title: MDA-MB-468 5mC5hmC, Control, 10 days, rep2

value: untreated


title: MDA-MB-468 5mC, DETA/NO, 10 days, rep1


title: AGI881_P1_D01, scRRBS (multi-omics)


title: AGI881_P1_D11, scRRBS (multi-omics)


title: Simurosertib1 (dataset 2)


title: IDHmut glioma, combo-1, Day9


title: AGI881_P1_D03, scRRBS (multi-omics)


title: AGI881_P1_C11, scRRBS (multi-omics)


title: MDA-MB-468 5mC, Control, 10 days, rep2


title: IDHmut glioma, veliparib-2, Day9

value: veliparib


title: Enzalutamide4 (dataset 2)

value: Prostate

value: Enzalutamide


title: MDA-MB-468 5mC5hmC, Control, 10 days, rep1


title: IDHmut glioma, veliparib-1, Day9


title: AGI881_P1_D10, scRRBS (multi-omics)


title: Enzalutamide3 (dataset 2)

value: DKO 22PC

value: Prostate adenocarcinoma


title: MDA-MB-468 5mC, Control, 10 days, rep1


title: IDHmut glioma, lenvatinib-3, Day9

value: lenvatinib


title: AGI881_P1_C09, scRRBS (multi-omics)

value: Yes


title: MDA-MB-231 5mC5hmC, DETA/NO, 10 days, rep2


title: AGI881_P1_C08, scRRBS (multi-omics)


title: Enzalutamide1 (dataset 2)

value: TP53/RB1 KO


title: MDA-MB-231 5mC, DETA/NO, 10 days, rep2


title: IDHmut glioma, lenvatinib-2, Day9

value: Brain

value: Glioma cells


title: Combo1 (dataset 2)

value: Enzalutamide+Simurosertib


title: IDHmut glioma, lenvatinib-1, Day9

value: IDH-mutant


title: MDA-MB-231 5mC5hmC, DETA/NO, 10 days, rep1

value: triple-negative breast cancer


title: AGI881_P1_D09, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: Control4 (dataset 2)

value: Control


title: IDHmut glioma, ctrl-3, Day9


title: AGI881_P1_C05, scRRBS (multi-omics)


title: Control3 (dataset 2)


title: AGI881_P1_C04, scRRBS (multi-omics)


title: IDHmut glioma, ctrl-2, Day9


title: Control2 (dataset 2)


title: Enzalutamide2 (dataset 2)


title: IDHmut glioma, ctrl-1, Day9


title: MDA-MB-231 5mC5hmC, Control, 10 days, rep2

value: epithelial


title: MDA-MB-231 5mC, Control, 10 days, rep2

value: untreated


title: AGI881_P1_D08, scRRBS (multi-omics)


title: AGI881_P1_C03, scRRBS (multi-omics)


title: Control1 (dataset 2)


title: Combo3

value: DKO LnCap/AR


title: Combo2

value: Prostate


title: MDA-MB-231 5mC5hmC, Control, 10 days, rep1


title: Combo1


title: AGI881_P1_C02, scRRBS (multi-omics)


title: MDA-MB-231 5mC, DETA/NO, 10 days, rep1

value: 100 uM DETA/NO


title: AGI881_P1_D06, scRRBS (multi-omics)


title: AGI881_P1_B12, scRRBS (multi-omics)


title: ARLA01and05, HTO

city: Würzburg

first: Johannes

last: Dirks

state: DE

address: Josef-Schneider-Straße 2

department: Pediatric Immunology

country: Germany

institute: University Hospital Julius-Maximilians University Würzburg

description: processed data available on GSE entry

data_processing:
Standard workflow of Cellranger-6.1.2 was used for mapping and counting.
Assembly: GRCh38-2020-A
Supplementary files format and content: Cell ranger output for gene expression matrixes and VDJ TCR sequencing.

source_name: Synovial fluid

extract_protocol:
Cd4+ SF T cells were einriched from SF mononuclear cells either by FAS sort (ARLA01 and 05) or enriched in CD4+ T cells using the EasySep™ Human CD4+ T Cell Isolation Kit (stemcell technologies, Vancouver, Canada, ARLA02).
The library for 5 ' scRNA and VDJ TCR sequencing was prepared following 10X genomics instructions. For ARLA01 and 05 a hashtag library was included: TotalSeqC Hashtag Oligos (Biolegend; ARLA01: GTCAACTCTTTAGCG, ARLA05: TTCCGCCTCTCTTTG).

value: Synovial fluid

value: T cells

tag: library type

value: HTO


title: ARLA02, VDJ

value: VDJ TCR


title: Simurosertib2

value: Prostate adenocarcinoma

value: TP53/RB1 KO

value: Simurosertib


title: Simurosertib3


title: ARLA02, scRNA

value: GEX 5'


title: Low-grade glioma, Vorinostat_3, Day37

city: Shanghai

first: Yeung

last: Sivannn

address: Dongan Road

institute: Fudan University

data_processing:
FastQC was used to filter out adapter and low-quality reads and Hisat2 was used  to aligned high-quality reads to mouse genome (mm10) .
Expression level of each gene was with default normalized by StringTie with Transcripts Per Kilobase (TPM) methods
Then we used SVA to remove confounder factors across all samples, and calculated differential expression genes between each two treatments using DESeq2.
Assembly: mm10
Supplementary files format and content: Processed data file is the gene expression profile as xlsx format. The expression value was processed as TPM for subsequent analysis.

growth_protocol: For stereotactic injection, DF-1 cells expressing WT or R132H-mutant IDH were mixed with DF-1 cells expressing PDGFB in a 1:1 ratio with the final concentration of 5×105/3μl. The mice were anesthetized with isoflurane, and a stereotactic device (Stoelting, catalog #51600) was used to locate the coordinates to the bregma, 2mm to the left and 3mm down on a dorsal view. Cells were injected at a speed of 0.4 µl/min with a pump using a 10 µm diameter needle. Brains of injected mice MR imaging was aquired at a 500-MHz Bruker 11.7T BioSpec 117/16 USR MRI system (Bruker BioSpin, Ettlingen, Germany). For mouse brain imaging, brain axial T2-weighted parameters are as followings: repetition time (TR)/echo time (TE) = 3500/10 ms, acquisition matrix = 256×256, NA = 2, field of view (FOV) = 32×32 mm, number of slices = 26, no gap, slice thickness = 0.8 mm, flip angle (FA) = 90°. MRI was performed at 28 days after DF-1 cell injection to determine tumor formation and size. Mice were then randomly assigned to start administration, all of which were administered by intraperitoneal injection.

extract_protocol:
The tumor samples were collected from IDH-mutant mice after 9 days treatments and cut into 1 mm3 with surgical blade. Samples were sent on ice to Benagen Technology Co., Ltd for immediate downstream RNA sequencing. In brief, following RNA isolation with Trizol (catalog #, check with Benagen), a total amount of 2 μg RNA per sample was used as input material for library preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences.

treatment_protocol: Vorinostat was administered by intraperitoneal injection of 100ul (1 mg/100ul in 10% DMSO, 45% PEG-300, 5% Tween-20, ddH2O) once per day. Anti-PD1 was administered by intraperitoneal injection of 1mg/100ul in PBS, twice per week. The control group was administered by placebo (10% DMSO, 45% PEG-300, 5% Tween-20, ddH2O) injection of 100ul once a day.

value: Brain

value: Low-grade glioma cells

value: IDH-mutant

value: Vorinostat


title: AGI881_P1_C01, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell

value: Yes


title: AGI881_P1_B05, scRRBS (multi-omics)


title: Low-grade glioma, Vorinostat_4, Day37


title: Simurosertib1

value: DKO LnCap/AR


title: AGI881_P1_B04, scRRBS (multi-omics)


title: ARLA01and05, scRNA

description: processed data available on GSE entry


title: ARLA01and05, VDJ


title: AGI881_P1_B03, scRRBS (multi-omics)


title: MDA-MB-231 5mC, Control, 10 days, rep1

value: triple-negative breast cancer

value: epithelial

value: untreated


title: Enzalutamide3

value: Prostate

value: Enzalutamide


title: C2984TIP

city: GUANGZHOU

first: PENG

last: SHEN

address: GUANGZHOUDADAOBEI 1838

institute: NANFANG HOSPITAL

description: For Merip-Seq

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
MeRIPseq reads were aligned to the hg38 genome using STAR.
m6A Peaks were called uing MetPeak  with the significance cut-off p-value <=0.05
Assembly: hg38
Supplementary files format and content: BED (except for Input sample)

source_name: colorectal cancer

extract_protocol: further transcriptome-wide interrogation was pursued by deep sequencing using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; Takara/Clontech, Japan) according to the manufacturer's protocol.

value: colorectal cancer

tag: merip antibody


title: Low-grade glioma, Ctrl_3, Day37

value: Control


title: Low-grade glioma, Ctrl_2, Day37


title: AGI881_P1_B01, scRRBS (multi-omics)


title: Enzalutamide2

value: Prostate adenocarcinoma

value: TP53/RB1 KO


title: C2984Tinput

description: For Merip-Seq


title: AGI881_P1_A12, scRRBS (multi-omics)


title: Enzalutamide1


title: C2984NIP

description: For Merip-Seq

source_name: adjacent normal

value: adjacent normal


title: Low-grade glioma, Ctrl_1, Day37

value: Brain


title: Low-grade glioma, Vorinostat_2, Day37

value: Low-grade glioma cells


title: Control3


title: C2984Ninput

description: For Merip-Seq


title: AGI881_P1_A11, scRRBS (multi-omics)


title: Control2


title: Low-grade glioma, Combination_4, Day37

value: IDH-mutant

value: anti-PD1 + Vorinostat


title: AGI881_P1_A09, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: HUDEP-2 mock transfected, clone 36, rep5

city: Seattle

first: Jeff

last: Vierstra

state: WA

address: 2211 Elliot Ave

institute: Altius Institute for Biomedical Sciences

data_processing:
Basecalling, RTA v3.4.4
Alignments to GRCh38, star v2.4.2a
Annotation, cufflinks v2.2.1, GENCODE v25
Subread, featureCounts v1.5.1
Assembly: GRCh38
Supplementary files format and content: featureCounts gene counts per sample as gzipped tab-delimited matrix

growth_protocol: HUDEP-2 were maintained in Iscove's modified Dulbecco's medium (IMDM) supplemented with 330 μg/mL human holo-transferrin (Sigma), 10 μg/mL recombinant human insulin (Sigma), 2 IU/mL heparin (Sigma), 5% human AB plasma (obtained from Bloodworks Northwest, Seattle, WA), 3 IU/mL EPO, 100 ng/mL SCF, 1 μg/mL doxycycline (Sigma), and 100 units/ml penicillin/streptomycin.

extract_protocol:
Approximately 200,000 cells were collected per culture and total RNA was isolated using QIAGEN RNeasy kit per manufacturer's instructions
RNA library was constructed using the Illumina RNA TruSeq Stranded tRNA with Ribo-Zero Globin

value: human erythroid progenitor

value: WT


title: C2978Tinput

description: For Merip-Seq


title: Low-grade glioma, Combination_3, Day37


title: H146-Cis4

value: :Lung

value: SCLC

value: Cisplatin


title: C2978TIP

description: For Merip-Seq


title: Low-grade glioma, Vorinostat_1, Day37

value: Vorinostat


title: Low-grade glioma, Combination_2, Day37


title: AGI881_P1_B09, scRRBS (multi-omics)

value: Yes


title: AGI881_P1_A06, scRRBS (multi-omics)


title: HUDEP-2 mock transfected, clone 36, rep2

value: untreated


title: Low-grade glioma, Combination_1, Day37


title: Low-grade glioma, antiPD1_4, Day37


title: HUDEP-2 mock transfected, clone 36, rep3


title: C2978Ninput

description: For Merip-Seq


title: HUDEP-2 mock transfected, clone 36, rep4


title: Low-grade glioma, antiPD1_3, Day37


title: C2978NIP

description: For Merip-Seq


title: AGI881_P1_B06, scRRBS (multi-omics)


title: C2957Tinput

description: For Merip-Seq

value: colorectal cancer


title: AGI881_P1_A01, scRRBS (multi-omics)


title: C2957TIP

description: For Merip-Seq


title: HUDEP-2 TL17275:TL17276 & TL17287:TL17288 transfected, clone 24, rep 5

value: PPARA DHS knockout


title: HUDEP-2 mock transfected, clone 36, rep1


title: C2957NIP

description: For Merip-Seq


title: IDHmut glioma, veliparib-3, Day9

value: Glioma cells

value: veliparib


title: Mouse Notch1-KO, DMSO treated, Chromium gene expression

description: Chromium_mouse_cell_line_processed_UMI.tsv

data_processing:
We used CellRanger (v4.0.0) with the default parameters. Gene expression matrices were generated using cellranger (count command) by aligning the FASTQ files to a reference transcriptome.
Assembly: GRCh38 for Homo sapiens, mm10 for Mus musculus
Supplementary files format and content: tsv

source_name: Mouse cell line single cell, IDHmutant mouse glioma cell NOTCH1 KO

extract_protocol:
Fresh specimens were mechanically dissociated with a disposable, sterile scalpel and further enzymatically dissociated into single cell suspensions using the enzymatic brain dissociation kit (papain-based) from Miltenyi Biotec as previously reported. Tumor cells were blocked in 1% bovine serum albumin in phosphate-buffered saline solution (1% BSA / PBS). Cell suspensions were subsequently stained for flow cytometry for 30 min at 4 °C using antibodies specific for CD45 [REA747]-VioBlue and CD3 [BW264/56]-PE from Miltenyi Biotec. Cells were washed with cold PBS, and then incubated for 15 min in 1.5 mL of 1% BSA / PBS containing 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies). Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter; CD3-PE, 585/42 filter), 640nm (TO-PRO-3, 670/14 filter), and 405 nm (CD45-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3. We sorted individual, viable, CD45+CD3- and CD45+CD3+ immune, and CD45- non-immune single cells into 96-well plates containing cold TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80 °C prior to whole transcriptome amplification, library preparation and sequencing. Frozen tumor tissue (approximately 5mm x 5mm x 5mm) was placed into a well of a 6-well plate (Corning, Cat. No. CLS3516-50EA) containing 1 ml of CST buffer and processed on ice. Tumor tissue was chopped for 10 minutes using Noyes Spring Scissors (Fine Science Tools, Cat. No. 15514-12). The sample was then filtered through a 40 um cell strainer (Fisher Scientific, Cat. No. 22363547) and the well and filter were washed with an additional 1 ml of CST buffer. The total volume was then brought up to 5 ml with 3 ml of ST buffer and the sample was centrifuged in a 15 ml conical tube at 4°C for 5 minutes at 500 g. The supernatant was removed and the pellet was resuspended in 100 ul ST buffer. The sample was then filtered through a 35 um cell strainer (Falcon, Cat. No. 352235). Nuclei suspension was counted using disposable C-Chip Hemocytometers (INCYTO, Cat. No. DHCN012). Single-nuclei were loaded on 10x genomics. IdhR132H mouse glioma cells with Notch1-KO and Notch1-WT were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks. The single-cell suspension for Notch1-KO and Notch1-WT mouse glioma cells treaded by AG-881 or DMSO (8,000 cells per group) were profiled by the 10X Chromium 3’ Single Cell Platform and were sequenced as already mentioned.
Single cells or single nucleus were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, 8,000 cells were added to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index.

value: No


title: Mouse Notch1-KO, IDHi treated, Chromium gene expression

value: Mouse cell line single cell, IDHmutant mouse glioma cell NOTCH1 KO


title: breast cells, E50K, Biological rep2

city: Atlanta

first: Jennifer

middle: Marie

last: Spangle

state: Georgia

address: 1365C Clifton Rd NE

institute: Emory University

data_processing:
Illumina Dragen was used to perform salmon quantification of transcript expression
Quantification was mapped to GRCh38
Assembly: hg38
Supplementary files format and content: the processed files are quant.sf that contain read counts

source_name: HMEC DD

growth_protocol: HMEC DD cells were maintained at 37C and 5% CO2 in DMEM/F12 media supplemented with 0.6% FBS, 0.01 µg/ml EGF, 10 µg/ml insulin, 0.025 µg/ml hydrocortisone, 1 ng/ml cholera toxin, 2.5 µg/ml Amphotericin B, and 1% Penicillin-Streptomycin

extract_protocol:
Total RNA was extracted from 80% confluent HMECDD cells overexpressing histone H3.3 WT or E50K using the RNAeasy Isolation kit (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: HMEC DD

value: Human mammary epithelial cells

value: no treatment


title: Low-grade glioma, antiPD1_1, Day37

value: Brain

value: Low-grade glioma cells

value: IDH-mutant


title: HUDEP-2 TL17275:TL17276 & TL17287:TL17288 transfected, clone 24, rep 3

value: human erythroid progenitor


title: Low-grade glioma, antiPD1_2, Day37


title: AGI881_P1_A08, scRRBS (multi-omics)

data_processing:
Analysis of single cell DNA methylation data was performed based on the methods detailed in Chaligne et al 2021. After demultiplexing, reads were mapped to the mm10 genome and cells with at least 25,000 CpG sites, 1 million reads and mapping efficiency greater than 30% were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: tsv

source_name: Mouse cell line single cell, IDHmutant mouse glioma cell

extract_protocol:
IdhR132H mouse glioma cells were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks.  The treated cells were washed with cold PBS and then stained with 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies) for 30 min at 4°C. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter) and  640nm (TO-PRO-3, 670/14 filter). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets. Calcein AM positive and TO-PRO-3 negative live cells were sorted into 96 wells containing TCL buffer (QIAGEN) for the single-cell multi-omics experiment.
The single-cell plates for the mouse glioma cells treaded by AG-881 or DMSO were profiled by the joint single-cell RRBS and whole transcriptome amplification (Smart-seq2) protocol. The library preparation and sequencing were performed as previously described (Chaligne et al, 2021). Single enzyme digestion (MspI) was used to enrich CpG dense regions in single-cell RRBS.


title: HUDEP-2 TL17275:TL17276 & TL17287:TL17288 transfected, clone 24, rep 4


title: C2957Ninput

description: For Merip-Seq

value: adjacent normal


title: Control1

data_processing:
In-line UMI sequences were trimmed from the sequencing reads with Marianas (https://github.com/mskcc/Marianas) and aligned to human GRCh38 genome using STAR 2.7.0 (https://github.com/alexdobin/STAR) [25] with Ensembl v92 gene annotation.
Hybrid selection-specific metrics and alignment metrics were calculated for the BAM files using CalculateHsMetrics and CollectRnaSeqMetrics, respectively, from Picard Toolkit (https://github.com/broadinstitute/picard) to determine the quality of the capture.
We quantified RNA-seq reads with Kallisto v.0.45.053 to obtain transcript counts and abundances.
Transcript per million (TPM) normalization by size factors was done from Kallisto output files using Sleuth v0.30.0 run in gene mode.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with TPM values over all genes for each sample.

extract_protocol:
Frozen tissues were weighed and homogenized in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water.
Fresh cell pellet or frozen tumor samples were shipped to GENEWIZ for RNA isolation, library preparation, and RNA sequencing. Total RNA was extracted using the RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). RNA samples and sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Sequencing libraries were clustered on one flowcell lane and then loaded on the Illumina HiSeq instrument (4000 or equivalent) (RRID: SCR_020127) according to manufacturer’s instructions. Samples were sequenced using a 2x150bp paired end (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bclfiles) was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software (RRID: SCR_015058). One mismatch was allowed for index sequence identification.

value: Prostate

value: DKO LnCap/AR

value: Prostate adenocarcinoma

value: TP53/RB1 KO

value: Control


title: AGI881_P1_A03, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell

value: Yes


title: breast cells, E50K, Biological rep1


title: breast cells, WT, Biological rep2

value: WT


title: HUDEP-2 TL17275:TL17276 & TL17287:TL17288 transfected, clone 24, rep 1

value: PPARA DHS knockout

value: untreated


title: GMPMAw3FP_4a

city: Columbus

first: Rodney

last: Britt

state: Oh

address: 575 Childrens Crossroad

department: Center for Perinatal Research

institute: Nationwide Children's Hospital

description: 10x genomics

data_processing:
10X Genomics cellranger-6.1.1 Single Cell 3' v3
Assembly: mm10-200-A
Supplementary files format and content: 10X Genomics cellranger-6.1.1 count tab-delimeted matrix and metadata files

source_name: Lung

extract_protocol:
Lung tissue was perfused with 5 mL cold sterile heparinized PBS by injection into the right ventricle. The lungs were then minced, placed in a Miltenyi C-tube containing digestion buffer (432 U/mL collagenase IV, 64 U/mL DNase), and then dissociated for 30 min on the Miltenyi Gentle MACS  OctoDissociator.  Samples were then filtered and prepared for Dead Cell removal (Miltenyi). Following dead cell removal, mouse immune cells were isolated using the CD45+ cell microbead isolation kit (Miltenyi) following manufacturer's instructions. After counting, single cell suspensions were prepared in cold buffer (1X PBS with 2% BSA).
The library was generated using the 10X genomics 3'-seq kit v3.1 following manufacturer's protocol. Single cells were captured using the Chromium Next GEM single cell 3’ Kit v3.1, 16 rxns PN-1000268, Chromium Next GEM Chip G Single Cell Kit, 48 rxns PN-1000120 and Dual Index Kit TT Set A, 96 rxns PN-1000215 (all from 10x Genomics) and run using Protocol CG000315 Rev C.

treatment_protocol: Starting on day 3-4 of life, newborn male and female mice were intranasally challenged with PBS or 0.5 ug c-di-GMP + mixed allergens (10 ug each: Dermatophagoides pteronyssinus (house dust mite), Aspergillus fumigatus, Alternaria alternata, ovalbumin) 3 times per week for 7 weeks. After 5 weeks mice were intraperitoneally injected with vehicle, 1 or 3 ,mg/kg fluticaone propionate (FP) 3 times per week during the last 2 weeks . Lungs were harvested the day after the last PBS or allergen challenged.

value: Lung

value: Homegenate

value: GMPMA 3FP


title: GMPMAw3FP_4b

description: 10x genomics


title: SeD, Room Air, PN3, Replicate 3

city: Oklahoma City

first: Abhrajit

last: Ganguly

state: Oklahoma

address: 800 Research Pkwy

department: Pediatrics

institute: University of Oklahoma Health Center

data_processing:
Quality check using FastQC
Trimming sequence length using trimmomatic setting LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:40
Mapping using HISAT2 with GRCm39 reference
Raw read count extracted by Featurecounts by setting --countReadPairs -s 2 -p
Normalization and differential test by DeSeq2
Differentially expressed genes with both Log2 folder change >|0.25| and adjust p value<0.05 were selected to further analysis.
Package clusterProfiler with R was used to conduct pathway analysis by using Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database.
Gene set enrichment analysis (GSEA) was conducted by using GSEA 4.1.0.
Assembly: mm39
Supplementary files format and content: sheet named "raw_count" in gene_expression.xlsx file denote raw count of genes in each sample
Supplementary files format and content: sheet named "filtered_normalized_count" in gene_expression.xlsx file denote normalization of genes in each sample
Supplementary files format and content: other sheets denote groupings for analysis.

extract_protocol:
RNA was isolated from the tissues using the Direct-Zol RNA miniprep kit and established protocols from Zymo Research (R2050S, Irvine, CA).
Stranded RNA-seq libraries were constructed using NEBNext poly(A) mRNA isolation kit followed directly by IDT’s XGen Broad Range RNA Library Prep Kit and the established protocols.

tag: dietary selenium_level

value: <0.01 ppm sodium selenite

tag: oxygen level

tag: age


title: Replicate F All GFP 15K lib transduced

data_processing:
Cloning region flanking sequences were trimmed using seqtk (https://github.com/lh3/seqtk) using the trimfq command and removing 22 bases from read1 and 20 from read2
Illumina adapters were trimmed using Trimmomatic v0.36 setting the ILLUMINACLIP argument to 2:30:10:2:true
Sequences were aligned against the GRCh38 reference genome with BWA and sequences were filtered using samtools with the following arguments: view -q 1 -f 64.
Sequences were converted to genomic coordinates BED file using the bam2bed tool from the BEDOPS suite
For every reference sequence (tile or full DHS depending on screening vector library) we counted the number of reads in each sample that overlap the reference sequence by ≥90% using the bedmap tool from BEDOPS.
Assembly: GRCh38
Supplementary files format and content: gzipped tab delimited table containing raw counts per tile across samples
Library strategy: DNAseq

extract_protocol:
Total DNA from enhancer screening library transduced HUDEP-2 cells was isolated using the DNeasy Blood & Tissue kit (Qiagen, 69504)
PCR amplicons indexed with Nextera dual indexes

value: human erythroid progenitors


title: GMPMAw1FP_3b

description: 10x genomics

tag: tissue

value: GMPMA 1FP


title: SeD, Room Air, PN3, Replicate 2


title: Mouse Notch1-WT, IDHi treated, Chromium gene expression

city: Charlestown

first: Masashi

last: Nomura

address: 149 13th street

institute: Massachusetts General Hospital

tag: treatment (idhi)


title: Replicate F GFP-Low 15K lib transduced

tag: cell line


title: DIPGXIII, RNA-seq, 72h after SB939, replicate 3

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

data_processing:
TPM
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each poly-A Sample [1-8]

extract_protocol:
RNA was isolated using RNeasy Plus Kit (Qiagen) according to manufacturer’s instructions and the quality was assessed with the Agilent 2100 Bioanalyzer with an RNA 6000 Pico Kit (Agilent Technologies).
PolyA-enriched RNA libraries were prepared with the KAPA Stranded mRNA Sample Preparation Kit (Kapa Biosystems).

value: brain

value: DIPGXIII

value: H3.3K27M mutant


title: GMPMAw1FP_3a

description: 10x genomics

tag: cell type


title: SeD, hyperoxia, PN3, Replicate 3


title: GMPMA_2b

description: 10x genomics

value: GMPMA


title: DIPGXIII, RNA-seq, 72h after SB939, replicate 1


title: Replicate F GFP-Medium 15K lib transduced


title: DIPGXIII, RNA-seq, 72h after SB939, replicate 2


title: SeD, hyperoxia, PN3, Replicate 2


title: DIPGXIII, RNA-seq, 48h after SB939, replicate 3


title: SeD, Room Air, PN3, Replicate 1


title: PBS_1b

description: 10x genomics

value: PBS


title: GMPMA_2a

description: 10x genomics


title: Replicate E All GFP 15K lib transduced


title: SeD, hyperoxia, PN3, Replicate 1


title: HUDEP-2 TL17275:TL17276 & TL17287:TL17288 transfected, clone 24, rep 2

value: human erythroid progenitor


title: Mouse Notch1-WT, DMSO treated, Chromium gene expression

value: Mouse cell line single cell, IDHmutant mouse glioma cell

value: No


title: DIPGXIII, RNA-seq, 48h after SB939, replicate 2


title: Replicate E GFP-Low 15K lib transduced

value: WT


title: breast cells, WT, Biological rep1

value: HMEC DD

value: Human mammary epithelial cells

value: no treatment


title: SeS, Room Air, PN3, Replicate 3

value: Lung

value: 0.4 ppm sodium selenite


title: PBS_1a

description: 10x genomics

value: Homegenate


title: DIPGXIII, RNA-seq, 48h after SB939, replicate 1


title: Replicate E GFP-Medium 15K lib transduced

value: human erythroid progenitors

value: untreated


title: ATAC_Th1_d3_KO_3

city: Bethesda

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

data_processing:
ATAC-seq reads from two biological replicates were mapped to the mouse genome (mm10 assembly) using Bowtie 45. Redundant reads were removed using FastUniq 46.
Customized Python scripts were used to calculate the fragment length of each pair of uniquely mapped paired-end (PE) reads. BigWig tracks were generated by HOMER 20 and visualized by IGV genome browser 47.
Assembly: mm10
Supplementary files format and content: bigwig files for ATAC-seq

source_name: Th1 cells

growth_protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.

extract_protocol:
Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
FastATAC-Seq was performed according to a published protocol(Corces et al., 2016) 10,000 sorted cells were pelleted and washed with 50 μl 1x PBS. After pelleting the nuclei by centrifuging at 500 x g for 10 minutes at 4°C, the pellets were re-suspended in 50 μl transposase mixture (25 μl of 2x TD buffer, 2.5 μl of TDE1, 0.5 μl of 1% digitonin, 22 μl of nuclease-free water) (Illumina, #20034197 and Promega, #G9441) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37°C with shaking at 300 rpm for 30 minutes.  The fragmentalized DNAs were then purified using a QIAGEN MinElute kit (Qiagen, #28006) and amplified with appropriate cycles of PCR based on the amplification curve using NEBNext High-Fidelity 2x PCR Master Mix (NEB, #M0541) and SYBR Green I (Thermo Fisher Scientific, #S-7563).
Once the libraries were purified using a QIAGEN PCR cleanup kit (Qiagen, #28106), they were further sequenced for 50bp paired-end reads on NovaSeq or NextSeq (Illumina).

treatment_protocol:
Wild type and IfngCTCFdel mice were inoculated with an average of 15 cysts of type II avirulent T. gondii strain ME-49 by intraperitoneal injection
LCMV (strain Armstrong) was thawed at 37°C and then injected into mice by intraperitoneal injection at the concentration 2 x 10^5 plaque-forming units (PFU) per mouse.

value: Spleen

tag: culture condition

value: ex vivo


title: DIPGXIII, RNA-seq, 16h after SB939, replicate 3

value: brain

value: DIPGXIII

value: H3.3K27M mutant

tag: treatment


title: SeS, Room Air, PN3, Replicate 2

tag: genotype


title: Replicate E GFP-High 15K lib transduced


title: SeS, Room Air, PN3, Replicate 1


title: ATAC_Th1_d3_KO_2


title: DIPGXIII, RNA-seq, 16h after SB939, replicate 2


title: Replicate F GFP-High 15K lib transduced


title: SKOV3 cells, ZIC2 KO biol rep 6

city: Edmonton

first: Laura

middle: Jiyoung

last: Lee

state: Alberta

address: 5-120 Katz Group Centre

department: Oncology

country: Canada

institute: University of Alberta

data_processing:
Sequence reads were trimmed for adaptor sequences using Skewer.
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR.
Gene-based read counts were obtained with FeatureCounts using aligned files generated with STAR.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw read counts for each sample.

growth_protocol: SKOV3 cells were cultured in DMEM/Hams’ F12 medium supplemented with 5% FBS. OVCAR3 cells were cultured in RMPI-1640 medium supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Qiagen RNeasy Mini Kit with on-column DNAse treatment. 1.5 ug of total RNA was submitted for library generation and sequencing.
RNA libraries for RNA-seq were generated using NEB mRNA stranded Library preparation.

value: ovarian cancer cells

value: ZIC2 knockout


title: SKOV3 cells, ZIC2 KO biol rep 5


title: SeD, Room Air, PN1, Replicate 3

value: <0.01 ppm sodium selenite


title: ATAC_Th1_d3_KO_1


title: ATAC_Th1_d3_WT_3


title: DIPGXIII, RNA-seq, 16h after SB939, replicate 1


title: SKOV3 cells, ZIC2 KO biol rep 4


title: SeS, hyperoxia, PN3, Replicate 3


title: ATAC_Th1_d3_WT_2


title: DIPGXIII, RNA-seq, 3h after SB939, replicate 3


title: DIPGXIII, RNA-seq, 3h after SB939, replicate 2


title: SeD, Room Air, PN1, Replicate 2


title: ATAC_Th1_d3_WT_1


title: SeS, hyperoxia, PN3, Replicate 2


title: DIPGXIII, RNA-seq, 3h after SB939, replicate 1


title: SKOV3 cells, ZIC2 KO biol rep 3


title: SeS, hyperoxia, PN3, Replicate 1


title: HiC_NK_KO

data_processing:
alignment: Hi-C sequencing reads from two biological replicates for each cell type and genotype were trimmed using HOMER, then mapped to the mouse genome (mm10) using Bowtie.
peaks: Hi-C tag directories were created using HOMER. And Hi-C interaction matrices were generated and normalized using HOMER with parameters -res 1000 -window 5000 -balance -corr. The interaction matrices were converted to .h5 files and visualized using HiCExplorer after merging the two biological replicates.
Supplementary files format and content: text or .h5 or .hic files for focuesed Hi-C.

source_name: NK cells

growth_protocol: in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.

extract_protocol:
cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
3-5 million cells were aliquoted from pooled naïve T cells or Th1 cells differentiated in vitro for each genotype, then pelleted and fixed with formaldehyde (1% v/v) for 5 minutes with mixing, before the reaction was quenched with glycine (0.2M). Cells were washed, pelleted, and flash frozen on dry ice for storage in -80°C before the Hi-C protocol was initiated. Global Hi-C was performed according to previously published protocols (Rao, 2014). After global Hi-C was completed, 500 ng of Hi-C libraries were used as the pond for the hybrid selection reaction. A 1,550,000 bp region surrounding the Ifng locus was hybridized using a collection of 2367 RNA probes. Local in situ Hi-C was performed according to previously published protocols.
DNA libraries were constructed according to to previously published protocols.
DNA libraries were sequenced at 100 million reads with 50bp paired-end reads using NovaSeq (Illumina).

treatment_protocol:
Toxoplasma gondii infection protocol: Wild type and IfngCTCFdel mice were inoculated with an average of 15 cysts of type II avirulent T. gondii strain ME-49 by intraperitoneal injection
LCMV infection protocol: LCMV (strain Armstrong) was thawed at 37°C and then injected into mice by intraperitoneal injection at the concentration 2 x 10^5 plaque-forming units (PFU) per mouse.

value: NK cells


title: SKOV3 cells, ZIC2 KO biol rep 1


title: HiC_NK_WT


title: SeS, Room Air, PN1, Replicate 3


title: DIPGXIII, RNA-seq, DMSO, replicate 2

value: DMSO


title: SKOV3 cells, ZIC2 WT biol rep 6

value: WT


title: Focused-HiC_Th1_D3_F_KO2

value: Th1 cells


title: SeS, Room Air, PN1, Replicate 2

value: Lung


title: DIPGXIII, RNA-seq, DMSO, replicate 1


title: SeD, hyperoxia, PN1, Replicate 3


title: Focused-HiC_Th1_D3_F_KO1


title: SeS, Room Air, PN1, Replicate 1

value: 0.4 ppm sodium selenite


title: H60_DSA_High_02

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60) and were mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation ( human release 31).
Assembly: GRCh38 (hg38)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

growth_protocol: Molm 14 cells were cultured in RPMI with 10% heat-inactivated FBS, L-glutamine and penn strep. HL-60 cells were cultured in IMDM with 20% heat-inactivated FBS, L-glutamine and penn strep. Both cell lines were maintained in 5% CO2 at 37oC.

extract_protocol:
Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: Molm 14 cells were cultured in growth media and treated with low (11.1 pM) and high (100 pM) concentrations of DSA for 36 hours. HL-60 cells were cultured in growth media with low (112.7 pM) and high (500 pM) concentrations of DSA for 36 hours.

value: human leukemia

value: High DSA for 36 hours


title: Focused-HiC_Th1_D3_F_WT2


title: SeD, hyperoxia, PN1, Replicate 2


title: Focused-HiC_Th1_D3_F_WT1


title: SKOV3 cells, ZIC2 WT biol rep 3


title: SKOV3 cells, ZIC2 WT biol rep 2


title: SeS, hyperoxia, PN1, Replicate 3


title: H60_DSA_Low_02

value: Low DSA for 36 hours


title: H60_DSA_Low_01


title: Focused-HiC_Naive_F_KO2

source_name: Naïve T cells

value: Spleen

value: Naive T cells


title: SKOV3 cells, ZIC2 WT biol rep 1


title: SKOV3 cells, ZIC2 KO biol rep 2


title: DIPGXIII, RNA-seq, DMSO, replicate 3

value: brain


title: SeD, hyperoxia, PN1, Replicate 1


title: Focused-HiC_Naive_F_KO1

value: ex vivo


title: H60_ctrl_02

value: no treatment


title: HEY_shPQBP1_3

city: Jinan

first: Xihan

last: Liu

state: Shandong

address: Wenhuaxi Road #44

institute: Shandong University

data_processing:
The total RNA quantity was analyzed by Agilent Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RNA integrity number (RIN) >7.0.
Poly-T oligo-attached magnetic beads were used to purify poly(A) mRNA by two rounds of purification. The mRNA is fragmented and reverse-transcribed to construct cDNA library according to the mRNASeq sample preparation kit protocol (Illumina, San Diego, USA)
After obtaining paired-end reads, clean reads were aligned to the hg38 genome with HISAT2 (version 2.2.0) and sorted with samtools (version 1.9).
Transcripts were reconstructed with StringTie (1.3.0)
differential expression was analyzed with edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HEY

extract_protocol:
Total RNA was extracted from cells by TRIzol reagent (Invitrogen) and then next-generation sequencing was performed by the LC-Bio.
The RNAseq library was paired-end sequenced using Illumina HiSeq 4000 at LC-Bio.

value: HEY

value: ovarian cancer cells

value: PQBP1 knockdown

value: Dox inducement (1 microg/ml)

tag: time

value: Day 3


title: Focused-HiC_Naive_F_WT2


title: SKOV3 cells, ZIC2 WT biol rep 5

value: WT


title: SeS, hyperoxia, PN1, Replicate 2


title: Focused-HiC_Naive_F_WT1


title: HEY_shPQBP1_2


title: SKOV3 cells, ZIC2 WT biol rep 4


title: H60_DSA_High_01


title: M14_DSA_High_02

value: acute myeloid leukemia


title: bulkRNA_Th1_D3_KO3_IFNg

description:
bulkRNA_Th1_D3_anti-gamma_IFNg_results.gene.rpkm.xlsx
bulkRNA_Th1_D3_anti-gamma_IFNg_results.gene.ANOVA.xlsx

data_processing:
alignment: The run was demultiplexed and converted to FastQ using bcl2fastq v2.20.0.422 (Illumina) and mapped to mm10 using Tophat 2.1.0.
FPKM: Partek Genomics Suite 7.0 (Partek) was used to calculate Reads Per Kilobase of transcript, per Million mapped reads (RPKM), perform analysis of variance (ANOVA) comparisons, perform principal component analysis (PCA) and perform hierarchical clustering.
Assembly: mm10
Supplementary files format and content: excel files for bulk RNA-seq

extract_protocol:
cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
Total RNA was extracted from 200,000 cells using QIAzol Lysis Reagent and the Direct-zol microprep RNA kit.
mRNA purification, cDNA synthesis and cDNA library preparation was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, #E7770) and NEBNext Multiplex Oligos for Illumina (NEB, #E6609).
cDNA libraries were sequenced at 20 million reads per sample with 50bp paired-end reads using NovaSeq or NextSeq (Illumina).


title: HEY_shPQBP1_1


title: HEY_shNC_3

value: NC


title: M14_DSA_High_01


title: SeS, hyperoxia, PN1, Replicate 1

value: Lung

value: 0.4 ppm sodium selenite


title: bulkRNA_Th1_D3_KO3_anti_gamma


title: PC isotype

first: David

last: Huang

address: 9000 Rockville Pike

institute: National Cancer Institute

description: FACS sorted murine plasma cells

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 human genome using BOTWIE2
Peaks were called by an inhouse program
Assembly: mm10
Supplementary files format and content: peak-read counts in wig format

source_name: spleen

growth_protocol: Mice were immunized on day0 and day7 with sheep red blood cells and euthanized for Cut&Run analysis 10 days after the first immunization.

extract_protocol:
DNA was extracted and processed following the Epicypher Cut&Run Kit protocol.
DNA libraries were prepared for sequencing using standard Epicypher protocols

treatment_protocol: Naive B cells, germinal center B cells and plasma cells were FACS sorted from the spleen of euthanized mice 10 days after initial immunization. Approximately 500 000 cells were used per Cut&Run reaction.

value: spleen

value: plasma cells

tag: antibody

value: control

value: no time course


title: bulkRNA_Th1_D3_KO3

tag: strain

value: Spleen


title: M14_DSA_Low_01

value: Low DSA for 36 hours


title: PC ARID1A 3

description: FACS sorted murine plasma cells

value: no treatment


title: SeD, Room Air, PN1, Replicate 1

value: <0.01 ppm sodium selenite


title: HEY_shNC_1

value: HEY

value: ovarian cancer cells


title: PC ARID1A 2

description: FACS sorted murine plasma cells


title: bulkRNA_Th1_D3_KO2_anti_gamma

value: ex vivo


title: CD8 EMRA T cell, chemerin binder, rep3

city: Palo Alto

first: Melissa

last: LaJevic

address: 3801 Miranda Ave

institute: PAVIR

description:
D-plus
normalized_counts.csv
Differential_expression_analysis_table.csv

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software. Raw sequence data generated from Illumina HiSeq was converted in fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.
Sequence reads were trimmed using Trimmomatic v.0.36 and mapped to the Homo Sapiens reference genome. BAM files were generated.
Unique gene hit counts were calculated by using feature Counts from the Subread package v1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 was used to compare gene expression between the groups (plus vs minus). The Wald test was used to generate P values and Log2 fold changes. Genes with adjusted P values <0.05 and absolute log2 fold changes >1 were called differentially expressed genes.
Assembly: Trimmed reads were mapped to the Homo Sapiens reference genome available on ENSEMBL (GRCh38.p13 (GCA_000001405.28)) using the STAR aligner v2.5.2b

source_name: blood

extract_protocol:
Chemerin-binding and non-binding blood CD8+ EMRA T cells (CD8+ CD45RO- CCR7-) were sorted from PBMCs from 3 donors by flow cytometry. RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA library preparations and sequencing reactions were conducted by Azenta US, Inc (South Plainfield, NJ, USA)
Library was prepared using SMART-Seq HT kit for full-length cDNA synthesis and amplification (Takara, San Jose, CA, USA), and Illumina Nextera XT (Illumina, San Diego, CA, USA) library was used for sequencing library preparation.
cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoScientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
Ultra low input RNA seq

value: blood

value: PBMC

tag: sorted cell type

value: CD8 EMRA T cell

tag: phenotype

value: chemerin binder


title: M14_ctrl_02

value: acute myeloid leukemia


title: bulkRNA_Th1_D3_KO2_IFNg


title: PC ARID1A 1

description: FACS sorted murine plasma cells


title: GCB isotype 2

description: FACS sorted murine germinal center B cells

value: germinal center B cells

value: contrrol


title: H60_ctrl_01

value: human leukemia


title: T, replicate3

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
RNAseq reads were aligned to the hg38 genome using STAR.
Read counts for individual gene of each sample were produced with HTSeq-count
Assembly: hg38
Supplementary files format and content: xls(gene expression of all sample)

source_name: colorectal cancer tissue

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: colorectal cancer tissue


title: bulkRNA_Th1_D3_KO1_IFNg


title: GCB isotype 1

value: spleen

value: control

value: no time course


title: CD8 EMRA T cell, chemerin nonbinder, rep3

description:
D-minus
normalized_counts.csv
Differential_expression_analysis_table.csv

value: chemerin nonbinder


title: CD8 EMRA T cell, chemerin binder, rep2

description:
C-plus
normalized_counts.csv
Differential_expression_analysis_table.csv


title: N, replicate3

source_name: non-cancerous tissue

value: non-cancerous tissue


title: bulkRNA_Th1_D3_KO2

value: Spleen


title: CD8 EMRA T cell, chemerin nonbinder, rep2

description:
C-minus
normalized_counts.csv
Differential_expression_analysis_table.csv


title: HEY_shNC_2

value: HEY

value: ovarian cancer cells

value: NC

value: Day 3


title: M14_DSA_Low_02

value: Low DSA for 36 hours


title: CD8 EMRA T cell, chemerin binder, rep1

description:
A-plus
normalized_counts.csv
Differential_expression_analysis_table.csv

value: blood

value: PBMC

value: CD8 EMRA T cell

value: chemerin binder


title: GCB ARID1A 3

value: germinal center B cells

value: no treatment


title: bulkRNA_Th1_D3_KO1

value: ex vivo


title: T, replicate2

value: colorectal cancer tissue


title: N, replicate2


title: GCB ARID1A 2

value: spleen

value: no time course


title: CD8 EMRA T cell, chemerin nonbinder, rep1

description:
A-minus
normalized_counts.csv
Differential_expression_analysis_table.csv

value: chemerin nonbinder


title: T, replicate1


title: PTA5

city: Callaghan

first: Ting

last: La

state: NSW

address: University Drive

country: Australia

institute: UON

data_processing:
cell ranger(version 5.0.0; 10 × Genomics, Pleasanton, CA) was used to process the raw data
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Parathyroid

growth_protocol: A group of clinical symptoms resulting from excess parathyroid hormone secretion due to primary lesions of parathyroid tissue, including hypercalcemia, increased renal calcium reabsorption and urinary phosphorus excretion, kidney stones, renal calcinosis, and increased resorption of cortical bone

extract_protocol:
the cells were resuspended in calcium- and magnesium-free PBS containing 0.04% BSA, followed by centrifugation at 300g for 5 min. The cells were then resuspended in 1mL of ice-cold red blood cell lysis buffer.and incubated at 4 °C for 10 min, followed by the addition of 10 ml of ice-cold PBS and centrifugation at 300g for 10 min. After resuspension, the sample was filtered with a 40-μm cell strainer. Cell viability was then determined using Trypan Blue staining with an automated cell counter.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Parathyroid adenoma resection

value: Parathyroid

tag: gender

value: female

tag: disease state

value: adenoma


title: GCB ARID1A 1


title: bulkRNA_Th1_D3_WT3_anti_gamma

value: Spleen


title: N, replicate1

value: non-cancerous tissue


title: bulkRNA_Th1_D3_WT3_IFNg


title: M14_ctrl_01

value: acute myeloid leukemia


title: bulkRNA_Th1_D3_WT3


title: PTA4

value: male


title: naive isotype 1

description: FACS sorted murine naive B cells

value: naive B cells

value: control


title: PTA3


title: naive ARID1A 2

description: FACS sorted murine naive B cells


title: bulkRNA_Th1_D3_KO1_anti_gamma


title: PTA2


title: PD03

city: Beijing

first: Zijie

last: Xu

state: Beijing

address: Haidian District, Huayuan Road 49

department: Sports Medicine Department

institute: Peking University Third Hospital

description: scRNA-seq

data_processing:
The sequence reads were mapped to the GRCH38 human reference genome using Cell Ranger 6.0.1 (10x Genomics)
Assembly: GRCH38
Supplementary files format and content: Matrix files of gene counts

source_name: bone marrow

extract_protocol:
Intraoperatively aspirate bone marrow tissue from the patient and transfer it into an EDTA-coated anticoagulant tube. The bone marrow samples were collected into heparin tubes and density gradient centrifugation was used to isolate bone marrow cells.
The single-cell RNA libraries were prepared using Chromium Single Cell 5’ Library and Gel Bead Kit.

value: bone marrow

tag: subject status

value: Recurrent Patellar Dislocation (RPD) patient


title: bulkRNA_Th1_D3_WT2_IFNg


title: naive ARID1A 1

description: FACS sorted murine naive B cells

value: no treatment


title: bulkRNA_Th1_D3_WT2_anti_gamma

value: ex vivo


title: bulkRNA_Th1_D3_WT2


title: PD01

description: scRNA-seq


title: bulkRNA_Th1_D3_WT1_IFNg


title: PTA1


title: [Liver] [Ethanol-fed + PCB 126] [Replicate 5]

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Sequencing was performed on an Illumina NextSeq 2000
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the GRCm39 reference assembly using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using GRCm39.106.gtf.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited file of HTSeq raw counts

source_name: Liver

extract_protocol:
Total RNA was extracted using the standard RNA-STAT60 and chloroform method. Samples were then treated with DNase, Amplification Grade I to digest single- and double-stranded DNA species. Finally, RNA samples were treated with RNAClean XP beads at a 1:1 volume ratio to further purify our samples to remove salts, dNTPs, and miscellaneous enzymes
The TruSeq Stranded mRNA Library Prep Kit (Illumina) was used for library construction

treatment_protocol: Male C57BL/6J mice were exposed to 0.2 mg/kg PCB126 or corn oil vehicle prior to ethanol feeding in the chronic-binge model.

value: Liver

tag: Sex

tag: diet

value: EtOH

tag: agent


title: naive isotype 2

description: FACS sorted murine naive B cells

tag: tissue

value: spleen

value: no time course


title: MPS cellculture, replicate 2

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

institute: University Medicine Greifswald

data_processing:
Quality control of the raw reads was performed with FastQ Screen (ver. 0.11.8, default parameters). The mapping was done with NextGenMap with default parameters for “--sensitive” in paired end mode. The annotated genetic features were counted by FeatureCounts.
DeSeq2 was used to compare the 2D versus 3D groups in triplicates for differential expression analysis. The size factor was estimated and the shrinkage of effect size was used for all genes annotated in the count table, based on the gtf file of Homo sapiens (ENSEMBL, GRCh38). In addition to the log2 fold-change, the adjusted p-values were calculated with DeSeq2  in default settings.
Supplementary files format and content: Counted reads on the gtf-file by FeatureCounts (gene_counting.csv)
Supplementary files format and content: list of DEGs based on the analysis of DESeq2 in the supplementary file (DEGs_2Dvs3D.xlsx)

source_name: Kidney

growth_protocol: Human renal proximal tubule epithelial cells (RPTEC) were culture in DMEM-12 media (ThermoFisher, Waltham , MA, USA)  supplemented with 10% fetal bovine serum (FBS), 1% Penicillin/Streptomycin, 4 pg/ml Triiodo-L-thyronine, 10ug/10ug/10ng/mL ITS, 32 ng/mL Hydrocortisone, 10 ng/mL human recombinant EGF. All supplements were obtained from Merck Lifesciences (Darmstadt, Germany) Before all assays the cells were maintained in culture at 37°C, 5% CO2 until reaching approximately 90% confluency upon visual inspection. For dynamic culture RPTEC were embeded in a matrix consisting of low density rat tail collagen type I crosslinked with Genipin.

extract_protocol:
Total RNA was extracted from 2D and MPS cultures using the  RNAeasy Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer specifications. For MPS cultures the collagen matrix, with embedded RPTEC tubules, was dissolved in RTL buffer prior to isolation with mini-spin columns. RNA quantity was evaluted usnig a NanoDrop 2000 (ThermoFisher)
Ribosomal RNA was depleted using the RiboZero Kit (Illumina Inc., San Diego, USA) according to the manufacturer’s instructions. Library preparation and Illumina dye sequencing was done by Novogene Europe(Cambridge, UK) using a  (Illumina Inc., San Diego, USA) was used for data acquisition.

treatment_protocol: 2D static cultures and MPS cultures were not subjected to chemical or pharmacological treatment. The difference between the experimenatl groups is the culture conditions. 2D static culture: 5 days in 6-well plate with culture media. MPS dynamic culture: 5 days in the TissUse Humimic chip2 microperfusion platform with re-circulating flow driven by a peristaltic pump at a frequency of 60Hz (1 pulsation per second)

value: Kidney

tag: cell line

value: RPTEC

value: primary

value: wildtype

value: 5 days dynamic culture with culture media reperfusion at 37 C, 5% CO2


title: bulkRNA_Th1_D3_WT1_anti_gamma

value: Spleen

tag: cell type


title: [Liver] [Ethanol-fed + PCB 126] [Replicate 4]

value: male


title: GenX20.2

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p14 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (≥|2.0|-fold and ≤5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Assembly: human genome assembly NCBI GRCh38.p14
Supplementary files format and content: TMM normalized log counts per million (log CPM) values for each Sample

source_name: testes

growth_protocol: Cells were plated in DMEM with 10% FBS and 1% L-glutamine and 1x-Antibiotic/antimycotic

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.

treatment_protocol: (cells) indicated PFOS or vehicle control for 4 days; (mice) dosed with indicated PFAS or vehicle control for 15 days

value: testes

value: normal testes

value: 20 mg/kg GenX


title: MPS cellculture, replicate 1


title: GenX20.3


title: [Liver] [Ethanol-fed + PCB 126] [Replicate 3]


title: bulkRNA_Th1_D3_WT1

tag: culture condition


title: 2D culture, replicate 3

tag: treatment

value: 5 days static culture at 37 C, 5% CO2


title: GenX20.1


title: PFOS_20mg.3

value: 20 mg/kg PFOS


title: PFOS_20mg.2


title: [Liver] [Ethanol-fed + PCB 126] [Replicate 6]


title: MPS cellculture, replicate 3

tag: genotype


title: Parietal cells, MGI0900 48hr

city: Houston

first: Jason

middle: C

last: Mills

state: TX

address: 1 Baylor Plaza

department: Gastroenterology

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Quality control for filtering, normalization, clustering, and differential expression analysis was conducted in Seurat/R (R studio Version 4.1.2-“Bird Hippie”; Seurat  v5)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gastric corpus epithelium

extract_protocol:
Fresh gastric corpus was harvested and mechanically dissociated in DMEM media+ Collagenase 1A while shaking at  37° for 30 minutes. Tissue was further dissociated chemically in 5-15 minutes at 37° in 0.05% trypsin-EDTA. The single cell suspension was passed through a 30µm filter, quantity and viability assessed with hematocytometer, and submitted to the Washington University Genome Technology Access Core (GTAC) in 0.04% BSA 1x PBS.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3.1 protocol, 10x Genomics GEX). Briefly, cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-13 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell  Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

treatment_protocol: Mice in experimental group were treated with diphtheria toxin (225ng/mouse) once a day for three days. Tissue was harvested at 36h, 48h, or 72h after final injection. Each timepoint contains both male and female mice

value: gastric corpus epithelium

value: Epithelium

value: Diphtheria-Toxin treated+ 48h recovery


title: PFOS_20mg.1


title: [Liver] [Ethanol-fed + PCB 126] [Replicate 2]

value: Liver

value: EtOH


title: Peritoneal metastasis 48

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

data_processing:
Alignment protocol to be described
Read counts were normalized to log transformed transcript per million (TPM) values
Assembly: GRCh38
Supplementary files format and content: tab delimited file containing count values for all samples
Supplementary files format and content: tab delimited file containing tpm values for all samples

source_name: peritoneal metastasis

extract_protocol:
RNA  was harvested from FFPE samples using the Qiagen AllPrep DNA/RNA Mini Kit following the manufacturer protocol
Library construction protocol to be described

value: CRC

value: peritoneal metastasis


title: Parietal cells, MGI0900 36hr

description: 10x Genomics

value: Diphtheria-Toxin treated+ 36h recovery


title: [Liver] [Ethanol-fed + Vehicle] [Replicate 6]

value: Vehicle


title: 2D culture, replicate 1

value: Kidney

value: RPTEC

value: primary

value: wildtype


title: Parietal cells, MGI0900 Control

description: 10x Genomics

value: Vehicle treated


title: [Liver] [Ethanol-fed + Vehicle] [Replicate 5]

value: male


title: 2D culture, replicate 2

value: 5 days static culture at 37 C, 5% CO2


title: [Liver] [Ethanol-fed + PCB 126] [Replicate 1]


title: Peritoneal metastasis 47


title: PFOS_5mg.2

value: testes

value: normal testes

value: 5 mg/kg PFOS


title: Peritoneal metastasis 46


title: [Liver] [Ethanol-fed + Vehicle] [Replicate 4]


title: PFOS_5mg.1


title: NPA, H3K36me3, ChIP

city: La Jolla

first: Mannix

last: Burns

email: mburns@salk.edu, mannixburns@gmail.com

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute

data_processing:
Reads were aligned to the mm10 genome using the STAR alignment tool (version 2.5.3).
Peaks were called against an input control using MACS2 callpeak with the default --broad settings
BigWig files were subsequently generated using the HOMER makeBigWig command.
Assembly: mm10
Supplementary files format and content: bw
Supplementary files format and content: peak files (except input)

extract_protocol:
Cells were crosslinked with 1% paraformaldehyde for 10 min at room temperature and quenched with 0.125 M glycine for 5 min. Quenched cells were washed twice with ice-cold PBS supplemented with protease inhibitors (Cell Signaling Technology). Cell pellets were mixed with provided buffers to isolate the nuclei which were then treated with 1-2 μl of micrococcal nuclease for 30 min at 37°C to digest DNA to the length of approximately 150-1000 bps followed by sonication with a focused ultrasonicator (Covaris).
Isolated ChIP DNA was library prepped using the NEBNext Ultra II DNA Library Prep Kit for Illumina in accordance with the manufacturer’s protocol

value: mouse melanoma cell line

tag: chip antibody


title: NPA+aKG, H3K36me3, ChIP

value: 3-NPA + aKG


title: [Liver] [Ethanol-fed + Vehicle] [Replicate 3]

value: Liver

value: EtOH


title: C.UT3

value: control


title: PD02

description: scRNA-seq

value: bone marrow

value: Recurrent Patellar Dislocation (RPD) patient


title: Parietal cells, MGI0900 72hr

description: 10x Genomics

value: gastric corpus epithelium

value: Epithelium

value: Diphtheria-Toxin treated+ 72h recovery


title: [Liver] [Ethanol-fed + Vehicle] [Replicate 2]

value: Vehicle


title: DMSO, H3K36me3, ChIP

value: DMSO